1. - The purpose of this study is to determine
the mechanism in which variation occurs
in different populations of Arabidopsis
lyrata and to identify gene loci
responsible for adaptation to serpentine
soil.
- Using bioinformatics specific genes loci
will be analyzed by comparing
sequences from different populations.
- Analyze DNA variation through PCR
amplification and sequencing.
- This study will allow us to gain a better
understanding about the mechanism in
which populations acquire genetic
variation.
Introduction
Arabidopsis lyrata is a member of the
Brasiccae family (O’Kane and Al-Shehbaz
1997) is a close relative to Arabidopsis
thaliana. A. lyrata is an outcrossing
perennial woes populations are
geographically isolated (Leinone et al. 09)..
This study look at genetic difference
between the different populations in order
to examine the effects of natural selection
and genetic drift on populations.
A. lyrata is a small plant that is found in
serpentine, granitic and sandy soil.
Serpentine soil has a high heavy metal
concentration and a low calcium to
magnesium ratio. It is a difficult
environment for plants to grow on, however
A. lyrata can thrive in serpentine soil.
The gene being analyzed in this study have
been identified as possible candidates for
serpentine adaptation by Turner et al. The
ANNAT1 gene is a protein coding genes
found on chromosome 1 (Turner et al.) It
codes for calcium depended membrane
binding proteins.
Acknowledgments
Methods
- Identify the location of genes on A. lyrata
using the A. thaliana genome provided
by NCBI.
- Use Google maps to location areas of
sandy, granitic and serpentine soils to
look for populations of A. lyrata (see map
below for list of populations).
- Amplify ANNAT1 and IREG loci from
extracted DNA using PCR.
- Analyze the sequences using Genius
Pro.
- Describe the DNA polymorphisms using
statistical analysis.
ConclusionsVariation in ANNAT1 gene
in Populations of Arabidopsis lyrata
Katherine Molloy’15 and John M. Braverman, S.J., Ph.D.
Department of Biology, Saint Joseph’s University, Philadelphia, PA
Goals
Results
The sequences fro the ANNAT1 gene were compared
between twelve individuals from two serpentine
populations, one granitic population, and one sandy
population. Across all populations the nucleotide
diversity, π was .00489. Across the two serpentine,
Pilot* and Nottingham, the nucleotide diversity was
.00219. Within the Pilot populations there was a
nucleotide diversity of .001.
There were multiple amino acid polymorphism in the
codon regions of the genes. At base pair 1,818 there is
a glutamate/aspartate polymorphism, with the
Glutamate codon genotype only present in all the
individuals from serpentine populations (Fig 1). At base
pair 1710 there were three genotypes present across
all populations. The none serpentine populations had a
glycine codon. Individuals from Pilot (serpentine) all
had and alanine codon. In the Nottingham populations
there were two genotypes, Alanine codon and
threonine codon (Fig 2). The Nottingham population
also displayed multiple phenotypes unique to there
population at base pair 1373; an alanine/serine
polymorphism (Fig 3).
In addition to codon regions, there were also multiple
polymorphism in no coding regions. One was an indel
(insertion/deletion) of three base pairs at 524, GAT is
present in individuals from granitic 12 and serpentine
Pilot (Fig 4).
Willisbrook
Preserve
ChesLen
Preserve
Nottingham
County Park
Pilot,
Maryland
Lock 12
Recreation Area
Granitic
Serpentine
This map show the location of
five different population of A.
lyrata that were used in this
study. Natural Lands Trust
Willisbrook Preserve, Malvern
PA. Natural Lands Trust
ChesLen Preserve,
Coatesville PA. Nottingham
County Park, Nottingham PA.
The Nature Conservancy
Piolot Serpentine Barren,
Cecil County MD. Lock 12
Recreation Area, Holtwood
PA.
Fig 3. 1373 Alanine/Serine
polymorphism.
Fig 1. 1818 Glutamate/Aspartate polymorphism. Fig 2. 1710 Glycine/Alanine/Threonine polymorphisms
Fig 4. 524 GAT indel.
The ANNAT1 gene shows less variation between different
serpentine soil populations than it does across
populations from different soil types. The conservation of
ANNAT1 alleles that are only present in serpentine
populations could indicate natural selection. However the
conservation could also be a result of genetic drift. The
codon polymorphism at 1818 may be an important amino
acid change in order for plants to thrive on serpentine soil.
Turner et all also identified a glutamate/aspartate
polymorphism as a possible candidate for adaption to
serpentine soil, glutamate being the serpentine
adaptation. However both glutamate and aspartate are
hydrophilic amino acids so the change may not alter gene
function. If the later is the case than the conservation
could be a result of genetic drift indicating that the
serpentine population are more closely related to one
another than to the granitic and sandy. Two alleles appear
at 1710 in serpentine populations and neither one is
present in granitic or sandy soil populations. There was
variation at this cite in the Nottingham population of A.
lyrata. This shows that there are multiple functioning
alleles for this cite the allows for survival in serpentine
soil. The Nottingham population also had a unique
genotype at 1374. The alanine phenotype was not
present in any of the other populations regardless of their
soil type. The Nottingham population has two alleles that
are not found in any other the other populations, this could
be an example of genetic isolation between populations.
The indle at 524 most likely does not effect gene function
because it does not change the amino acids sequence of
the gene. However it is present in two different
populations. The chances of the same indle occurring by
change is so small that it is most likely due to a common
ancestry. The Lock 12 and Pilot populations both lie
along the Susquehanna river. There may be a geographic
linked between the two populations to explain the genetic
links between the two populations. Further study will look
into the gene function of ANNAT1 in addition to continuing
analysis of the genetic sequence.
Turner, T.L., Bourne, E.C., Von Wettberg, E.J., Hu, T.T., and Nuzhdin, S.V.
2010. Population Resequencing Reveals Local Adaptation of Arabidopsis lyrata
to Serpentine Soils. Nature Genetics 42, 260-263.
Leinone, Paivi H. Sandring, Saskia. Quilot, Benedicte. Clauss, Maria J. Mitchel-
Olds, Thomas. Agren, Jon. Savolainen, Outi. Local Adaptation in European
Populations of Arabidopsis lyrata (Brassicaceae). American Journal of Botany
96(6): 1129-1137. 2009.
O’Kane, Jr., S.L., Al-Shehbaz, I.A., 1997. A Synopsis of Arabidopsis
(Brassicaceae). Novon 7, 323–327.
*Two individuals grown the lab were grown from seeds from the Pilot population.